Docjar: A Java Source and Docuemnt Enginecom.*    java.*    javax.*    org.*    all    new    plug-in

Quick Search    Search Deep

org.biomage.Description
Class OntologyEntry  view OntologyEntry download OntologyEntry.java

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Description.OntologyEntry
All Implemented Interfaces:
org.biomage.Interface.HasOntologyReference, org.biomage.Interface.HasPropertySets, java.io.Serializable

public class OntologyEntry
extends org.biomage.Common.Extendable
implements java.io.Serializable, org.biomage.Interface.HasOntologyReference

A single entry from an ontology or a controlled vocabulary. For instance, category could be 'species name', value could be 'homo sapiens' and ontology would be taxonomy database, NCBI.


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasPropertySets
org.biomage.Interface.HasPropertySets.PropertySets_list
 
Field Summary
(package private)  java.lang.String category
          The category to which this entry belongs.
(package private)  java.lang.String description
          The description of the meaning for this entry.
private  DatabaseEntry ontologyReference
          Many ontology entries will not yet have formalized ontologies.
(package private)  java.lang.String value
          The value for this entry in this category.
 
Fields inherited from class org.biomage.Common.Extendable
 
Constructor Summary
OntologyEntry()
          Default constructor.
OntologyEntry(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 java.lang.String getCategory()
          Get method for category
 java.lang.String getDescription()
          Get method for description
 DatabaseEntry getOntologyReference()
          Get method for ontologyReference
 java.lang.String getValue()
          Get method for value
 void setCategory(java.lang.String category)
          Set method for category
 void setDescription(java.lang.String description)
          Set method for description
 void setOntologyReference(DatabaseEntry ontologyReference)
          Set method for ontologyReference
 void setValue(java.lang.String value)
          Set method for value
 void writeAssociations(java.io.Writer out)
          writeAssociations
 void writeAttributes(java.io.Writer out)
          writeAttributes
 void writeMAGEML(java.io.Writer out)
          writeMAGEML
 
Methods inherited from class org.biomage.Common.Extendable
addToPropertySets, addToPropertySets, getFromPropertySets, getPropertySets, removeElementAtFromPropertySets, removeFromPropertySets, setPropertySets
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

category

java.lang.String category
The category to which this entry belongs.


value

java.lang.String value
The value for this entry in this category.


description

java.lang.String description
The description of the meaning for this entry.


ontologyReference

private DatabaseEntry ontologyReference
Many ontology entries will not yet have formalized ontologies. In those cases, they will not have a database reference to the ontology. In the future it is highly encouraged that these ontologies be developed and ontologyEntry be subclassed from DatabaseReference.

Constructor Detail

OntologyEntry

public OntologyEntry()
Default constructor.


OntologyEntry

public OntologyEntry(org.xml.sax.Attributes atts)
Attribute constructor. Looks up the attributes in the parameter and casts them from strings appropriately

Method Detail

writeMAGEML

public void writeMAGEML(java.io.Writer out)
                 throws java.io.IOException
writeMAGEML

This method is responsible for assembling the attribute and association data into XML. It creates the object tag and then calls the writeAttributes and writeAssociation methods.


writeAttributes

public void writeAttributes(java.io.Writer out)
                     throws java.io.IOException
writeAttributes

This method is responsible for assembling the attribute data into XML. It calls the super method to write out all attributes of this class and it's ancestors.


writeAssociations

public void writeAssociations(java.io.Writer out)
                       throws java.io.IOException
writeAssociations

This method is responsible for assembling the association data into XML. It calls the super method to write out all associations of this class's ancestors.


setCategory

public void setCategory(java.lang.String category)
Set method for category


getCategory

public java.lang.String getCategory()
Get method for category


setValue

public void setValue(java.lang.String value)
Set method for value


getValue

public java.lang.String getValue()
Get method for value


setDescription

public void setDescription(java.lang.String description)
Set method for description


getDescription

public java.lang.String getDescription()
Get method for description


setOntologyReference

public void setOntologyReference(DatabaseEntry ontologyReference)
Set method for ontologyReference

Specified by:
setOntologyReference in interface org.biomage.Interface.HasOntologyReference

getOntologyReference

public DatabaseEntry getOntologyReference()
Get method for ontologyReference

Specified by:
getOntologyReference in interface org.biomage.Interface.HasOntologyReference